[English] 日本語
Yorodumi
- PDB-2yie: Crystal structure of a F. nucleatum FMN riboswitch bound to FMN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yie
TitleCrystal structure of a F. nucleatum FMN riboswitch bound to FMN
Components(FMN RIBOSWITCH) x 2
KeywordsRNA
Function / homologyFLAVIN MONONUCLEOTIDE / : / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.941 Å
AuthorsVicens, Q. / Mondragon, E. / Batey, R.T.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Molecular Sensing by the Aptamer Domain of the Fmn Riboswitch: A General Model for Ligand Binding by Conformational Selection
Authors: Vicens, Q. / Mondragon, E. / Batey, R.T.
History
DepositionMay 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: FMN RIBOSWITCH
Z: FMN RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,11119
Polymers36,2362
Non-polymers87517
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9541 Å2
ΔGint-87.4 kcal/mol
Surface area16104 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.679, 73.679, 139.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
RNA chain , 2 types, 2 molecules XZ

#1: RNA chain FMN RIBOSWITCH /


Mass: 17575.324 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 2495-2544 / Mutation: YES / Source method: obtained synthetically / Details: APTAMER DOMAIN BOUND TO FLAVIN MONONUCLEOTIDE
Source: (synth.) FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM (bacteria)
References: GenBank: 20095250
#2: RNA chain FMN RIBOSWITCH /


Mass: 18661.000 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 2550-2601 / Mutation: YES / Source method: obtained synthetically / Details: APTAMER DOMAIN BOUND TO FLAVIN MONONUCLEOTIDE
Source: (synth.) FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM (bacteria)
References: GenBank: 20095250

-
Non-polymers , 4 types, 46 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN X, A 2542 TO U ENGINEERED RESIDUE IN CHAIN X, G 2543 TO C ENGINEERED ...ENGINEERED RESIDUE IN CHAIN X, A 2542 TO U ENGINEERED RESIDUE IN CHAIN X, G 2543 TO C ENGINEERED RESIDUE IN CHAIN X, U 2544 TO C ENGINEERED RESIDUE IN CHAIN Z, C 2550 TO G ENGINEERED RESIDUE IN CHAIN Z, U 2551 TO A

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 64 %
Description: DATA WAS COLLECTED BY ANNIE HEROUX AS PART OF THE MACROMOLECULAR CRYSTALLOGRAPHY RESEARCH RESOURCE AT BROOKHAVEN NSLS
Crystal growDetails: RNA WAS CRYSTALLIZED FROM 15% PEG-MONOMETHYL 550 ETHER, 0.1 M MGCL2, 0.05 M NA-HEPES PH 7.0, 1 MM FMN

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 17834 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 80.36 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.7
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F2Q

3f2q


Resolution: 2.941→26.292 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 24.5 / Stereochemistry target values: ML
Details: THE GAMMA PHOSPHATE OF GTP IS DISORDERED ON CHAINS X AND Z
RfactorNum. reflection% reflection
Rfree0.2314 507 5.3 %
Rwork0.2041 --
obs0.2056 9559 98.03 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.744 Å2 / ksol: 0.247 e/Å3
Displacement parametersBiso mean: 96.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.6226 Å20 Å20 Å2
2---6.6226 Å20 Å2
3---13.2451 Å2
Refinement stepCycle: LAST / Resolution: 2.941→26.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2394 47 29 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032730
X-RAY DIFFRACTIONf_angle_d0.6124261
X-RAY DIFFRACTIONf_dihedral_angle_d24.2231379
X-RAY DIFFRACTIONf_chiral_restr0.056556
X-RAY DIFFRACTIONf_plane_restr0.005112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9415-3.36640.32161650.26392919X-RAY DIFFRACTION97
3.3664-4.23840.22041630.20053006X-RAY DIFFRACTION99
4.2384-26.29330.21621790.19113127X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24941.1174-0.01518.319-1.47550.25620.15551.94020.7914-0.440.30061.92850.2892.2825-0.3170.7305-0.12470.29522.3537-0.37351.51536.8853-62.881-58.7253
20.9540.22470.06320.84020.2470.8198-0.18550.2348-0.2243-0.01930.21020.00480.7215-0.3192-0.0660.7719-0.0698-0.05540.7859-0.01580.553427.305-58.91-71.5769
33.7990.5282-0.50771.2131.03562.57290.065-0.75871.4197-0.0356-0.12160.495-0.41350.24920.00350.3626-0.05850.07990.3714-0.10830.461228.935-44.7541-80.8539
41.8644-1.0002-0.03411.2484-1.23050.96810.0874-0.07090.1701-0.24820.03790.05020.41920.1422-0.0150.7615-0.00360.02740.67620.01370.625818.5514-76.1059-75.6039
50.20930.15470.50021.82120.4870.79060.1665-0.2261-0.7776-0.07-0.39981.25330.225-0.98750.02730.69220.1598-0.02141.02120.07791.3457-0.6527-65.4455-77.1439
66.07765.32350.16295.36551.30982.13740.40440.06910.93321.5368-1.11051.89590.27760.7149-0.08451.0770.3964-0.11890.6860.00821.3655-13.1103-46.4331-81.9627
71.9703-2.876-1.32835.13773.26572.5708-1.19270.4362-0.15831.297-0.1911.3605-0.19840.09590.62832.440.2883-0.19850.96250.12941.4851-11.8801-48.8534-75.1036
82.19322.1280.18822.26520.01760.15011.0522-0.6011-0.47990.3017-0.6791-0.41020.0693-0.197-0.06140.62660.1358-0.29541.24540.16381.2216-5.4727-61.0906-84.3032
90.5725-0.2901-0.28450.92940.75360.7896-0.1864-0.03-0.06530.32390.03770.02250.52850.27470.09160.75290.1533-0.05590.6518-0.00810.61622.8874-80.1053-86.2377
101.0551-0.94150.14430.3412-0.03660.4629-0.03130.30740.07620.24940.230.0142-0.01620.0313-0.05420.51350.0952-0.08190.4858-0.07170.484524.9118-80.7683-82.2455
111.86360.433-1.40780.40780.16181.80020.0629-0.20220.0868-0.04230.1609-0.092-0.49230.0467-0.14120.6710.05250.03060.66370.00370.713.7694-54.3297-74.3904
123.11160.6692-2.22740.6152-0.35021.62840.639-1.4264-0.67530.17150.47210.4956-0.2259-0.97460.440.5309-0.0750.3221.35530.27450.6862.0883-70.7748-57.4857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN Z AND RESID 57:61)
2X-RAY DIFFRACTION2(CHAIN Z AND RESID 62:66)
3X-RAY DIFFRACTION3(CHAIN Z AND RESID 67:78)
4X-RAY DIFFRACTION4(CHAIN Z AND RESID 79:98)
5X-RAY DIFFRACTION5(CHAIN Z AND RESID 99:106)
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 107:113)
7X-RAY DIFFRACTION7(CHAIN X AND RESID 1:5)
8X-RAY DIFFRACTION8(CHAIN X AND RESID 6:9)
9X-RAY DIFFRACTION9(CHAIN X AND RESID 10:19)
10X-RAY DIFFRACTION10(CHAIN X AND RESID 20:32)
11X-RAY DIFFRACTION11(CHAIN X AND RESID 33:48)
12X-RAY DIFFRACTION12(CHAIN X AND RESID 49:54)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more